Deep Genomics: It's time for a paradigm shift in medicine

Toronto, Ontario firm aims to become the world's first AI-based medicine company

"Medicine has always been hypothesis-driven," says Brendan Frey, Co-founder and CEO of Deep Genomics. "You wonder what's wrong, or whether a certain treatment will work, and then you do tests and experiments in order to receive a yes/no answer. That approach has yielded a lot of low-hanging fruit, but it won't work anymore. Going into the future, we need AI systems that can use huge amounts of data to pinpoint diseases and treatments."

A pioneer in deep learning

Early in his professional life, Frey studied neural networks and graphical models under Geoffrey Hinton at the University of Toronto, where he went on to make pioneering contributions to deep learning applications for image and speech recognition.

Then Frey and his wife at the time faced a family tragedy involving their unborn child. "It was very difficult to deal with emotionally," he recalls. "We were told that it could be nothing or it could be catastrophic. That's not good enough. We should have systems that can tell us what is likely to happen and to help us identify what the options are...No one should have to be in the position we were in." He decided the only way forward was to dedicate himself to impacting society in a profound way through the application of deep learning to medicine, and so in 2002, he changed the direction of his group to focus on how DNA encodes life.

Trying to connect the dots

"Despite the successes of the genome project, the 1,000 genome project and the 100,000 genome project... just because we can read the letters that make up the genome, it doesn't mean we know what it means," explains Frey. "If you can identify a mutation you learn that a certain nucleotide is different, but you don't know whether that's good, bad, or whether it can be fixed."

Frey believes artificial intelligence will provide the only way forward to understanding how the genome works, and will unlock insights that will drive the next generation of medicine. "No human and no group of humans will ever understand how the genome works - it's just too complex," states Frey. "We evolved to be good at vision, we invented language, we invented writing, but we did not evolve to read DNA. When you have a complex system with exponentially growing data there is only one solution and that's AI."

The light at the end of the tunnel

Deep Genomics' has already achieved considerable success, and they're on course for a moonshot. "By 2014, our deep learning systems were able to classify mutations as pathogenic or non-pathogenic, even though the system had never seen those mutations before," states Frey. For the past two years, Deep Genomics ran on C$5M in seed funding, but now Frey and his team are looking to raise C$15M. "What we'll do next is to take the current system and flip it on its head...We're aiming to become the world's first AI-based medicine company that can unlock new medicines."